| # cython: language_level=3 | |
| from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile | |
| ################################################# | |
| # Compatibility Layer for pysam < 0.8 | |
| # import all declarations from htslib | |
| from pysam.libchtslib cimport * | |
| cdef class AlignedRead(AlignedSegment): | |
| pass | |
| cdef class Samfile(AlignmentFile): | |
| pass | |
| # import the conversion functions | |
| cdef extern from "htslib_util.h": | |
| # add *nbytes* into the variable length data of *src* at *pos* | |
| bam1_t * pysam_bam_update(bam1_t * b, | |
| size_t nbytes_old, | |
| size_t nbytes_new, | |
| uint8_t * pos) | |
| # now: static | |
| int aux_type2size(int) | |
| char * pysam_bam_get_qname(bam1_t * b) | |
| uint32_t * pysam_bam_get_cigar(bam1_t * b) | |
| uint8_t * pysam_bam_get_seq(bam1_t * b) | |
| uint8_t * pysam_bam_get_qual(bam1_t * b) | |
| uint8_t * pysam_bam_get_aux(bam1_t * b) | |
| int pysam_bam_get_l_aux(bam1_t * b) | |
| char pysam_bam_seqi(uint8_t * s, int i) | |
| uint16_t pysam_get_bin(bam1_t * b) | |
| uint8_t pysam_get_qual(bam1_t * b) | |
| uint8_t pysam_get_l_qname(bam1_t * b) | |
| uint16_t pysam_get_flag(bam1_t * b) | |
| uint32_t pysam_get_n_cigar(bam1_t * b) | |
| void pysam_set_bin(bam1_t * b, uint16_t v) | |
| void pysam_set_qual(bam1_t * b, uint8_t v) | |
| void pysam_set_l_qname(bam1_t * b, uint8_t v) | |
| void pysam_set_flag(bam1_t * b, uint16_t v) | |
| void pysam_set_n_cigar(bam1_t * b, uint32_t v) | |
| void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) | |